Technische Universität Berlin, Chair of Bioanalytics, 10623, Berlin, Germany.
Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
Mol Syst Biol. 2024 Sep;20(9):1076-1084. doi: 10.1038/s44320-024-00057-2. Epub 2024 Aug 2.
Crosslinking mass spectrometry is a powerful tool to study protein-protein interactions under native or near-native conditions in complex mixtures. Through novel search controls, we show how biassing results towards likely correct proteins can subtly undermine error estimation of crosslinks, with significant consequences. Without adjustments to address this issue, we have misidentified an average of 260 interspecies protein-protein interactions across 16 analyses in which we synthetically mixed data of different species, misleadingly suggesting profound biological connections that do not exist. We also demonstrate how data analysis procedures can be tested and refined to restore the integrity of the decoy-false positive relationship, a crucial element for reliably identifying protein-protein interactions.
交联质谱是一种强大的工具，可在复杂混合物中研究天然或近天然条件下的蛋白质-蛋白质相互作用。通过新的搜索控制，我们展示了如何偏向于可能正确的蛋白质会微妙地破坏交联错误估计，从而产生重大影响。如果不进行调整来解决这个问题，我们在 16 次分析中平均错误识别了 260 种种间蛋白质-蛋白质相互作用，这些分析中我们混合了不同物种的数据，错误地暗示了不存在的深刻的生物学联系。我们还展示了如何测试和改进数据分析程序，以恢复诱饵-假阳性关系的完整性，这是可靠识别蛋白质-蛋白质相互作用的关键要素。
